Pythium irregulare vs Bigelowiella natans Translated Blat Results

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Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Pythium irregulare was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 7,577

Genome coverage (bp) Coding exon coverage (bp)
Pythium irregulare DAOM BR486

Uncovered: 42,133,987 out of 42,968,084
Covered: 834,097 out of 42,968,084

Uncovered: 19,761,076 out of 20,543,058
Matches: 523,982 out of 20,543,058
Mismatches: 257,850 out of 20,543,058
Insertions: 150 out of 20,543,058

Bigelowiella natans CCMP2755

Uncovered: 94,028,451 out of 94,701,163
Covered: 672,712 out of 94,701,163

Uncovered: 28,170,615 out of 28,817,508
Matches: 433,317 out of 28,817,508
Mismatches: 213,540 out of 28,817,508
Insertions: 36 out of 28,817,508

Configuration parameters

ParameterValue
Minimum score (minScore)30
Database type (t)dnax
Query type (q)dnax
Mask out repeats (mask)lower
Mask out repeats on query (qMask)lower

Chunking parameters

Pythium irregulare Bigelowiella natans
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}